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Parallel jobs with MPI and hands on tutorial

Parallel jobs with MPI and hands on tutorial. Enol Fernández del Castillo Instituto de Física de Cantabria. Introduction. What is a parallel job? A job that uses more than one CPU simultaneously to solve a problem Why go parallel? Save time Solve larger problems

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Parallel jobs with MPI and hands on tutorial

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  1. Parallel jobs with MPIand hands on tutorial Enol Fernández del Castillo Instituto de Física de Cantabria

  2. Introduction • What is a parallel job? • A job that uses more than one CPU simultaneously to solve a problem • Why go parallel? • Save time • Solve larger problems • Limits of hardware (speed, integration limits, economic limits) Curso Grid & e-Ciencia. Valencia - Julio 2010.

  3. Introduction • How? • Shared memory: all CPUs access a common data area • Message Passing: CPUs interchange messages with the data CPU CPU CPU Memory Mem Mem Mem CPU CPU CPU Interconn. Network Curso Grid & e-Ciencia. Valencia - Julio 2010.

  4. Introduction • Speed up: how fast the parallel version is. Curso Grid & e-Ciencia. Valencia - Julio 2010.

  5. Introduction • Shared Memory Model • Tasks share a common address space, which they read and write asynchronously. • Various mechanisms such as locks / semaphores may be used to control access to the shared memory. • No need to specify explicitly the communication of data between tasks. Program development can often be simplified. Curso Grid & e-Ciencia. Valencia - Julio 2010.

  6. Introduction • Message Passing Model • Tasks that use their own local memory during computation. • Multiple tasks can reside on the same physical machine as well across an arbitrary number of machines. • Tasks exchange data through communications by sending and receiving messages. • Data transfer usually requires cooperative operations to be performed by each process. For example, a send operation must have a matching receive operation. • MPI (Message Passing Interface) is an API for programming Message Passing parallel applications Curso Grid & e-Ciencia. Valencia - Julio 2010.

  7. Before MPI • Every computer manufacturer had his own programming interface • Pro • Offers the best performance on the specific system • Contra • Sometimes required to have in depth knowledge of the underlying hardware • Programmer has to learn different programming interfaces and paradigms (e.g. Shared memory vs. distributed memory) • Not portable • Efforts needs to be redone for every application port to a new architecture Curso Grid & e-Ciencia. Valencia - Julio 2010.

  8. MPI • Defines uniform and standard API (vendor neutral) for message passing • Allows efficient implementation • Provides C, C++ and Fortran bindings • Several MPI implementations available: • From hardware providers (IBM, HP, SGI….) optimized for their systems • Academic implementations • Most extended implementations: • MPICH (from ANL/MSU), includes support for a wide range of devices (even using globus from communication) • Open MPI (join effort from FT-MPI, LA-MPI, LAN/MPI and PACX-MPI developers): modular implementation that allows the use of advanced hardware during runtime Curso Grid & e-Ciencia. Valencia - Julio 2010.

  9. MPI-1 & MPI-2 • MPI-1 (1994) standardincludes: • Pointtopointcommunication • Collectiveoperations • Processgroupsandtopologies • Communicationcontexts • Datatype Management • MPI-2 (1997) adds: • DynamicProcess Management • File I/O • OneSidedCommunicactions • ExtensionofCollectiveOperations Curso Grid & e-Ciencia. Valencia - Julio 2010.

  10. Processes • Every MPI job consist of N processes • 1 <= N , N == 1 is valid • Each process in a Job could execute a different binary • In general it's always the same binary which executes different code path based on the process number • Processes are included in groups Curso Grid & e-Ciencia. Valencia - Julio 2010.

  11. Groups • A group is an ordered set of processes • Every process in a group has an unique rank inside the group • From 0 to #PROCS -1 • Processes can have different ranks in different groups • Groups are defined with MPI Communicators group X group Z A B C C B 0 1 2 0 1 Curso Grid & e-Ciencia. Valencia - Julio 2010.

  12. Hello World #include <mpi.h>    /* for MPI functions */ #include <stdio.h>  /* for printf */ int main(int argc, char *argv[] { int rank = 0, size = 0; MPI_Init(&argc, &argv); MPI_Comm_size(MPI_COMM_WORLD, &size); MPI_Comm_rank(MPI_COMM_WORLD, &rank); printf("Hello my rank is %i of %i\n", rank, size); MPI_Finalize(); return 0; } Curso Grid & e-Ciencia. Valencia - Julio 2010.

  13. Hello World • MPI_Init • initialize the MPI system • must be called before any other MPI function can be called • MPI_Comm_size • return the number of processes in the processes group • MPI_COMM_WORLD is a default group with all processes • MPI_Comm_rank • return the rank of the current process in the group • MPI_Finalize • Shutdown the MPI system • After this call MPI must not be called Curso Grid & e-Ciencia. Valencia - Julio 2010.

  14. Hello World #include <mpi.h>    /* for MPI functions */ #include <stdio.h>  /* for printf */ int main(int argc, char *argv[] { int rank = 0, size = 0; MPI_Init(&argc, &argv); MPI_Comm_size(MPI_COMM_WORLD, &size); MPI_Comm_rank(MPI_COMM_WORLD, &rank); printf("Hello my rank is %i of %i\n", rank, size); MPI_Finalize(); return 0; } Hello my rank is 2 of 5 Hello my rank is 1 of 5 Hello my rank is 0 of 5 Hello my rank is 4 of 5 Hello my rank is 3 of 5 Curso Grid & e-Ciencia. Valencia - Julio 2010.

  15. Communication between processes • Two types of processes communication: • Point-to-point: the source process knows the rank of the destination process and sends message directed to it. • Collective: all the processes in the group are involved in the communication. • Most functions are blocking. That is: the process waits until it has received completely the message. Curso Grid & e-Ciencia. Valencia - Julio 2010.

  16. Point-to-point • MPI_Send: int MPI_Send(void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm) • When MPI_Send return it means that the user can safely re-use the buffer, but not that the send operation already completed of even that the remote process received the data • MPI_Recv: int MPI_Recv(void *buf, int count, MPI_Datatype datatype,  int source, int tag, MPI_Comm comm, MPI_Status *status) • When MPI_Recv return the data has been received into the specified buffer (check status for possible errors) Curso Grid & e-Ciencia. Valencia - Julio 2010.

  17. Point-to-point: ring example #include <mpi.h> #include <stdio.h> int main(int argc, char *argv[]) { MPI_Status status; MPI_Request request; int rank = 0, size = 0; int next = 0, prev = 0; int data = 0; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &size); prev = (rank + (size­1)) % size; next = (rank + 1) % size; MPI_Send(&rank, 1, MPI_INT, next, 0, MPI_COMM_WORLD); MPI_Recv(&data, 1, MPI_INT, prev, 0, MPI_COMM_WORLD, &status); printf("%i received %i\n", rank, data);     MPI_Finalize();      return 0; } 0 1 2 Curso Grid & e-Ciencia. Valencia - Julio 2010.

  18. Collective Operations Curso Grid & e-Ciencia. Valencia - Julio 2010.

  19. Collective Operations Example int main(int argc,char *argv[]) { int n, myid, numprocs, i; double mypi, pi, h, sum, x; MPI_Init(&argc,&argv); MPI_Comm_size(MPI_COMM_WORLD,&numprocs); MPI_Comm_rank(MPI_COMM_WORLD,&myid); n = 10000; /* default # of rectangles */ MPI_Bcast(&n, 1, MPI_INT, 0, MPI_COMM_WORLD); h = 1.0 / (double) n; sum = 0.0; for (i = myid + 1; i <= n; i += numprocs) { x = h * ((double)i - 0.5); sum += 4/(1+x*x); } mypi = h * sum; MPI_Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD); if (myid == 0) { printf("pi is approximately %.16f\n", pi); } MPI_Finalize(); return 0; } Curso Grid & e-Ciencia. Valencia - Julio 2010.

  20. Take into account… • MPI is no Magic: • “I installed XXX-MPI in 3 of my machines but my Photoshop doesn't run faster !?!” • MPI is not an implementation • MPI is not the holy grail • Some problems don't really fit into the message passing paradigm • It's quite easy to write a parallel MPI application that perform worse than the sequential version • MPI works fine on shared memory systems, but maybe an OpenMP solution would work better Curso Grid & e-Ciencia. Valencia - Julio 2010.

  21. Some MPI resources • MPI Forum http://www.mpi-forum.org/ • Open MPI http://www.open-mpi.org/ • MPICH (2)http://www.mcs.anl.gov/research/projects/mpich2/ • MPI Tutorials: • http://www2.epcc.ed.ac.uk/computing/training/document_archive/mpi-course/mpi-course.book_1.html • https://computing.llnl.gov/tutorials/mpi/ Curso Grid & e-Ciencia. Valencia - Julio 2010.

  22. Moving to the grid… • There is no standard way of starting an MPI application • No common syntax for mpirun, mpiexec support optional • The cluster where the MPI job is supposed to run doesn't have a shared file system • How to distribute the binary and input files? • How to gather the output? • Different clusters over the Grid are managed by different Local Resource Management Systems (PBS, LSF, SGE,…) • Where is the list of machines that the job can use? • What is the correct format for this list? • How to compile MPI program? • How can a physicist working on Windows workstation compile his code for/with an Itanium MPI implementation? Curso Grid & e-Ciencia. Valencia - Julio 2010.

  23. MPI-Start • Specify a unique interface to the upper layer to run a MPI job • Allow the support of new MPI implementations without modifications in the Grid middleware • Support of “simple” file distribution • Provide some support for the user to help manage his data GridMiddleware MPI-START MPI Resources Curso Grid & e-Ciencia. Valencia - Julio 2010.

  24. MPI-Start design goals • Portable • The program must be able to run under any supported operating system • Modular and extensible architecture • Plugin/Component architecture • Relocatable • Must be independent of absolute path, to adapt to different site configurations • Remote “injection” of mpi-start along with the job • “Remote” debugging features Curso Grid & e-Ciencia. Valencia - Julio 2010.

  25. MPI-Start architecture CORE Scheduler Execution Hooks Local User Compiler File Dist. Open MPI MPICH2 LAM PACX PBS/Torque SGE LSF Curso Grid & e-Ciencia. Valencia - Julio 2010.

  26. MPI-Start flow START Scheduler Plugin NO Do we have a scheduler plugin for the current environment? Ask Scheduler plugin for a machinefile in default format NO Execution Plugin Do we have a plugin for the selected MPI? Activate MPI Plugin Prepare mpirun Trigger pre-run hooks Start mpirun Trigger post-run hooks Hooks Plugins Dump Env EXIT Curso Grid & e-Ciencia. Valencia - Julio 2010.

  27. Using MPI-Start • Interface with environment variables: • I2G_MPI_APPLICATION: • The executable • I2G_MPI_APPLICATION_ARGS: • The parameters to be passed to the executable • I2G_MPI_TYPE: • The MPI implementation to use (e.g openmpi, ...) • I2G_MPI_VERSION: • Specifies which version of the the MPI implementation to use. If not defined the default version will be used Curso Grid & e-Ciencia. Valencia - Julio 2010.

  28. Using MPI-Start • More variables: • I2G_MPI_PRECOMMAND • Specifies a command that is prepended to the mpirun (e.g. time). • I2G_MPI_PRE_RUN_HOOK • Points to a shell script that must contain a “pre_run_hook” function. • This function will be called before the parallel application is started (usage: compilation of the executable) • I2G_MPI_POST_RUN_HOOK • Like I2G_MPI_PRE_RUN_HOOK, but the script must define a “post_run_hook” that is called after the parallel application finished (usage: upload of results). Curso Grid & e-Ciencia. Valencia - Julio 2010.

  29. Using MPI-Start • The script: • The submission (in SGE): • The StdOut: • The StdErr: • MPI commands are transparent to the user • No explicit mpiexec/mpirun instruction • Start the script via normal LRMS submission [imain179@i2g-ce01 ~]$ cat test2mpistart.sh #!/bin/sh # This is a script to show how mpi-start is called # Set environment variables needed by mpi-start export I2G_MPI_APPLICATION=/bin/hostname export I2G_MPI_APPLICATION_ARGS= export I2G_MPI_NP=2 export I2G_MPI_TYPE=openmpi export I2G_MPI_FLAVOUR=openmpi export I2G_MPI_JOB_NUMBER=0 export I2G_MPI_STARTUP_INFO=/home/imain179 export I2G_MPI_PRECOMMAND=time export I2G_MPI_RELAY= export I2G_MPI_START=/opt/i2g/bin/mpi-start # Execute mpi-start $I2G_MPI_START [imain179@i2g-ce01 ~]$ qsub -S /bin/bash -pe openmpi 2 -l allow_slots_egee=0 ./test2mpistart.sh [imain179@i2g-ce01 ~]$ cat test2mpistart.sh.o114486 Scientific Linux CERN SLC release 4.5 (Beryllium) Scientific Linux CERN SLC release 4.5 (Beryllium) lflip30.lip.pt lflip31.lip.pt [lflip31] /home/imain179 > cat test2mpistart.sh.e114486 Scientific Linux CERN SLC release 4.5 (Beryllium) Scientific Linux CERN SLC release 4.5 (Beryllium) real 0m0.731s user 0m0.021s sys 0m0.013s Curso Grid & e-Ciencia. Valencia - Julio 2010.

  30. PRACTICAL SESSION… Curso Grid & e-Ciencia. Valencia - Julio 2010.

  31. Get the examples • wget http://devel.ifca.es/~enol/mpi.tgz • tar xzf mpi.tgz Curso Grid & e-Ciencia. Valencia - Julio 2010.

  32. parallel-job.jdl JobType = "Normal"; nodeNumber = 4; Executable = "starter.sh"; Arguments = "hello.sh OPENMPI"; InputSandbox = {"starter.sh", "hello.sh"}; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; Requirements = Member("MPI-START”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && Member("OPENMPI”, other.GlueHostApplicationSoftwareRunTimeEnvironment); Curso Grid & e-Ciencia. Valencia - Julio 2010.

  33. starter.sh #!/bin/bash MY_EXECUTABLE=$1 MPI_FLAVOR=$2 # Convert flavor to lowercase for passing to mpi-start. MPI_FLAVOR_LOWER=`echo $MPI_FLAVOR | tr '[:upper:]' '[:lower:]'` # Pull out the correct paths for the requested flavor. eval MPI_PATH=`printenv MPI_${MPI_FLAVOR}_PATH` # Ensure the prefix is correctly set. Don't rely on the defaults. eval I2G_${MPI_FLAVOR}_PREFIX=$MPI_PATH export I2G_${MPI_FLAVOR}_PREFIX # Touch the executable. It exist must for the shared file system check. # If it does not, then mpi-start may try to distribute the executable # when it shouldn't. touch $MY_EXECUTABLE # chmod +x $MY_EXECUTABLE # Setup for mpi-start. export I2G_MPI_APPLICATION=$MY_EXECUTABLE #export I2G_MPI_APPLICATION_ARGS="./ 0 0 1" export I2G_MPI_TYPE=$MPI_FLAVOR_LOWER # optional hooks #export I2G_MPI_PRE_RUN_HOOK=hooks.sh #export I2G_MPI_POST_RUN_HOOK=hooks.sh # If these are set then you will get more debugging information. #export I2G_MPI_START_VERBOSE=1 #export I2G_MPI_START_TRACE=1 #export I2G_MPI_START_DEBUG=1 # Invoke mpi-start. $I2G_MPI_START Curso Grid & e-Ciencia. Valencia - Julio 2010.

  34. hello.sh #!/bin/bash echo "hello world from `hostname`” Curso Grid & e-Ciencia. Valencia - Julio 2010.

  35. List-match $ glite-wms-job-list-match -a job.jdl Connecting to the service https://wms01.egee.cesga.es:7443/glite_wms_wmproxy_server ========================================================================== COMPUTING ELEMENT IDs LIST The following CE(s) matching your job requirements have been found: *CEId* - gridce01.ifca.es:2119/jobmanager-sge-ngifor - ngiesce.i3m.upv.es:2119/jobmanager-pbs-ngies - ce2.egee.cesga.es:2119/jobmanager-lcgsge-GRID_ngifor ========================================================================== Curso Grid & e-Ciencia. Valencia - Julio 2010.

  36. Submission $ glite-wms-job-submit –a job.jdl Connecting to the service https://wms01.egee.cesga.es:7443/glite_wms_wmproxy_server ====================== glite-wms-job-submit Success ====================== The job has been successfully submitted to the WMProxy Your job identifier is: https://wms01.egee.cesga.es:9000/q5BP68lwwUH4-YFzrgHBhQ ========================================================================== glite-wms-job-status https://wms01.egee.cesga.es:9000/q5BP68lwwUH4-YFzrgHBhQ ======================= glite-wms-job-status Success ===================== BOOKKEEPING INFORMATION: Status info for the Job : https://wms01.egee.cesga.es:9000/q5BP68lwwUH4-YFzrgHBhQ Current Status: Running Status Reason: Job successfully submitted to Globus Destination: gridce01.ifca.es:2119/jobmanager-sge-ngifor Submitted: Tue Jul 6 10:12:19 2010 CEST ========================================================================== Curso Grid & e-Ciencia. Valencia - Julio 2010.

  37. Output $ glite-wms-job-output https://wms01.egee.cesga.es:9000/q5BP68lwwUH4-YFzrgHBhQ Connecting to the service https://wms01.egee.cesga.es:7443/glite_wms_wmproxy_server ================================================================================ JOB GET OUTPUT OUTCOME Output sandbox files for the job: https://wms01.egee.cesga.es:9000/q5BP68lwwUH4-YFzrgHBhQ have been successfully retrieved and stored in the directory: /gpfs/csic_projects/grid/tmp/jobOutput/enol_q5BP68lwwUH4-YFzrgHBhQ ================================================================================ $ cat /gpfs/csic_projects/grid/tmp/jobOutput/enol_q5BP68lwwUH4-YFzrgHBhQ/* hello world from gcsic142wn hello world from gcsic142wn hello world from gcsic142wn hello world from gcsic142wn Curso Grid & e-Ciencia. Valencia - Julio 2010.

  38. Debugging • Use the MPI-START debugging variables: • Basic information: • I2G_MPI_START_VERBOSE=1 • Debug information: • I2G_MPI_START_DEBUG=1 • Full trace of the execution: • I2G_MPI_START_TRACE=1 • Set them in the starter.sh or in the JDL: Environment = {“I2G_MPI_START_VERBOSE=1”,…} Curso Grid & e-Ciencia. Valencia - Julio 2010.

  39. Debugging output ************************************************************************ UID = ngifor080 HOST = gcsic177wn DATE = Tue Jul 6 12:07:15 CEST 2010 VERSION = 0.0.66 ************************************************************************ mpi-start [DEBUG ]: dump configuration mpi-start [DEBUG ]: => I2G_MPI_APPLICATION=hello.sh mpi-start [DEBUG ]: => I2G_MPI_APPLICATION_ARGS= mpi-start [DEBUG ]: => I2G_MPI_TYPE=openmpi […] mpi-start [INFO ]: search for scheduler mpi-start [DEBUG ]: source /opt/i2g/bin/../etc/mpi-start/lsf.scheduler mpi-start [DEBUG ]: checking for scheduler support : sge mpi-start [DEBUG ]: checking for $PE_HOSTFILE mpi-start [INFO ]: activate support for sge mpi-start [DEBUG ]: convert PE_HOSTFILE into standard format mpi-start [DEBUG ]: dump machinefile: mpi-start [DEBUG ]: => gcsic177wn.ifca.es mpi-start [DEBUG ]: => gcsic177wn.ifca.es mpi-start [DEBUG ]: => gcsic177wn.ifca.es mpi-start [DEBUG ]: => gcsic177wn.ifca.es mpi-start [DEBUG ]: starting with 4 processes. Curso Grid & e-Ciencia. Valencia - Julio 2010.

  40. Compilation using hooks #!/bin/sh pre_run_hook () { # Compile theprogram. echo "Compiling ${I2G_MPI_APPLICATION}" # Actually compile theprogram. cmd="mpicc ${MPI_MPICC_OPTS} -o ${I2G_MPI_APPLICATION} ${I2G_MPI_APPLICATION}.c" $cmd if [ ! $? -eq 0 ]; then echo "Error compilingprogram. Exiting..." exit 1 fi # Everything's OK. echo "Successfullycompiled ${I2G_MPI_APPLICATION}" return 0 } Curso Grid & e-Ciencia. Valencia - Julio 2010.

  41. Compilation using hooks JobType = "Normal"; nodeNumber = 4; Executable = "starter.sh"; Arguments = ”cpi OPENMPI"; InputSandbox = {"starter.sh", “cpi.c”, “hooks.sh”}; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; Requirements = Member("MPI-START”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && Member("OPENMPI”, other.GlueHostApplicationSoftwareRunTimeEnvironment); Environment = {“I2G_MPI_PRE_RUN_HOOK=hooks.sh”}; Curso Grid & e-Ciencia. Valencia - Julio 2010.

  42. Compilation using hooks […] mpi-start [DEBUG ]: Try to run pre hooks at hooks.sh mpi-start [DEBUG ]: call pre_run hook -<START PRE-RUN HOOK>------------------------------------------- Compiling cpi Successfully compiled cpi -<STOP PRE-RUN HOOK>-------------------------------------------- […] =[START]======================================================== […] pi is approximately 3.1415926539002341, Error is 0.0000000003104410 wall clock time = 0.008393 =[FINISHED]====================================================== Curso Grid & e-Ciencia. Valencia - Julio 2010.

  43. Getting ouput using hooks […] MPI_Comm_rank(MPI_COMM_WORLD,&myid); […] char filename[64]; snprintf(filename, 64, "host_%d.txt", myid); FILE *out; out = fopen(filename, "w+"); if (!out) fprintf(stderr,"Unable to open %s!\n", filename); else fprintf(out, "Partial pi result: %.16f\n", mypi); […] Curso Grid & e-Ciencia. Valencia - Julio 2010.

  44. Getting ouput using hooks #!/bin/sh export OUTPUT_PATTERN="host_*.txt" export OUTPUT_ARCHIVE=myout.tgz # the first paramter is the name of a host in the copy_from_remote_node() { if [[ $1 == `hostname` || $1 == 'hostname -f' || $1 == "localhost" ]]; then echo "skip local host" return 1 fi CMD="scp –r $1:\"$PWD/$OUTPUT_PATTERN\" .” $CMD } post_run_hook () { echo "post_run_hook called" if [ "x$MPI_START_SHARED_FS" == "x0" -a "x$MPI_SHARED_HOME" != "xyes" ] ; then echo "gather output from remote hosts" mpi_start_foreach_host copy_from_remote_node fi echo "pack the data" tar cvzf $OUTPUT_ARCHIVE $OUTPUT_PATTERN return 0 } Curso Grid & e-Ciencia. Valencia - Julio 2010.

  45. Getting ouput using hooks JobType = "Normal"; nodeNumber = 4; Executable = "starter.sh"; Arguments = ”cpi2 OPENMPI"; InputSandbox = {"starter.sh", “cpi2.c”, “hooks.sh”}; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; Requirements = Member("MPI-START”, other.GlueHostApplicationSoftwareRunTimeEnvironment) && Member("OPENMPI”, other.GlueHostApplicationSoftwareRunTimeEnvironment); Environment = {“I2G_MPI_PRE_RUN_HOOK=hooks.sh”, “I2G_MPI_PRE_RUN_HOOK=hooks.sh”}; Curso Grid & e-Ciencia. Valencia - Julio 2010.

  46. Getting ouput using hooks […] mpi-start [DEBUG ]: Try to run post hooks at hooks.sh mpi-start [DEBUG ]: call post-run hook -<START POST-RUN HOOK>------------------------------------------- post_run_hook called pack the data host_0.txt host_1.txt host_2.txt host_3.txt -<STOP POST-RUN HOOK>-------------------------------------------- Curso Grid & e-Ciencia. Valencia - Julio 2010.

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